RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6808
(132 letters)
>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding
protein, retroviral integration, preintegration
complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB:
1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A
Length = 89
Score = 85.3 bits (211), Expect = 4e-23
Identities = 30/41 (73%), Positives = 38/41 (92%)
Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDK 68
M+TSQKH++FV+EPMGEKPV LAG+G+VLGK+LE +GFDK
Sbjct: 1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDK 41
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 516
Score = 28.3 bits (63), Expect = 0.87
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 8/44 (18%)
Query: 5 PTHWCNSTV--------HFWPFTSPTQELAKMSTSQKHQNFVSE 40
P H S+V H + T L + S S K+ + E
Sbjct: 373 PLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQE 416
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family
DNA polymerase, translesion DNA synthesis, lesion
bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7
PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
Length = 459
Score = 28.0 bits (62), Expect = 0.87
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 10/57 (17%)
Query: 20 SPTQELAKM-STSQK---------HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGF 66
+P LAK+ S K ++ V + + + P+ +++G+G V K L++ G
Sbjct: 247 APNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGI 303
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA
repair, DNA synthesis, binding, magnesium,
metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens}
Length = 504
Score = 27.5 bits (61), Expect = 1.4
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 20 SPTQELAKM-STSQK-------HQNFVSEPMGEKPVTELAGVGDVLGKRLESKG 65
LA+M + K V + + + VT L GVG + +L S G
Sbjct: 282 GSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLG 335
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.5 bits (60), Expect = 1.8
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 11/53 (20%)
Query: 55 DVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKN----PNSLPIPIGV-EVL 102
V +L + + S+N +P K +F P S IP + ++
Sbjct: 349 HVNCDKLTTI-IESSLNVL---EPAEYRK--MFDRLSVFPPSAHIPTILLSLI 395
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding
nucleotide binding M binding, nucleus; HET: DNA TTD DTP;
3.34A {Homo sapiens}
Length = 517
Score = 26.9 bits (59), Expect = 2.1
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 10/57 (17%)
Query: 20 SPTQELAKM-STSQK---------HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGF 66
+P LAK+ S K ++ V + + + P+ +++G+G V K L++ G
Sbjct: 303 APNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGI 359
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
Length = 150
Score = 26.3 bits (59), Expect = 2.3
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 6/26 (23%)
Query: 47 VTELAGVGDVLGKRLESKGFDKSINP 72
V ELAG+ D+L K S G S P
Sbjct: 114 VLELAGISDILSK---SIG---SNTP 133
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
Length = 162
Score = 26.3 bits (59), Expect = 2.6
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 46 PVTELAGVGDVLGKRLESKGFDKSINP 72
+ ELAGV D+L K G S NP
Sbjct: 108 AILELAGVTDILTK---ELG---SRNP 128
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
3i1z_E 3i21_E 3izv_I* 3izw_I* 3kc4_E 3or9_E 3ora_E
3sfs_E* 3uoq_E*
Length = 167
Score = 26.4 bits (59), Expect = 2.8
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINP 72
M + V E+AGV +VL K + G S NP
Sbjct: 110 AM--RAVLEVAGVHNVLAK---AYG---STNP 133
>3r8n_E 30S ribosomal protein S5; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_E 3fih_E* 3iy8_E 2wwl_E 3oar_E 3oaq_E
3ofb_E 3ofa_E 3ofp_E 3ofx_E 3ofy_E 3ofo_E 3r8o_E 4a2i_E
2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E ...
Length = 150
Score = 25.9 bits (58), Expect = 2.9
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 6/26 (23%)
Query: 47 VTELAGVGDVLGKRLESKGFDKSINP 72
V E+AGV +VL K + G S NP
Sbjct: 105 VLEVAGVHNVLAK---AYG---STNP 124
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 308
Score = 26.4 bits (58), Expect = 3.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 47 VTELAGVGDVLGKRLESK 64
V E+AGV + LGK+L S
Sbjct: 256 VLEMAGVENALGKQLGSN 273
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 25.3 bits (54), Expect = 5.6
Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 7/29 (24%)
Query: 23 QELAKMSTSQKHQNFVSEPMGEKPVTELA 51
Q L K+ S K + P LA
Sbjct: 20 QALKKLQASLK----LYAD-DSAPA--LA 41
Score = 24.9 bits (53), Expect = 8.3
Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 23/45 (51%)
Query: 59 KRLESKGFDKSINPQMF-PD--PDIEEKVLLFKNPNSLPIPIGVE 100
K+L++ S+ +++ D P +L I +E
Sbjct: 23 KKLQA-----SL--KLYADDSAP-------------ALAIKATME 47
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA;
heptameric ring, heptamer, ring, oligomer, RAD51
polymerizat motif; HET: DNA; 2.85A {Pyrococcus
furiosus} SCOP: a.60.4.1 c.37.1.11
Length = 349
Score = 25.7 bits (56), Expect = 5.6
Identities = 9/45 (20%), Positives = 20/45 (44%)
Query: 23 QELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFD 67
+EL +++ + + + +L GVG ++L G+D
Sbjct: 13 EELGFEPATEETPKKKKKEKIIRSIEDLPGVGPATAEKLREAGYD 57
>1xo8_A AT1G01470; structural genomics, protein structure initiative,
center for eukaryotic structural genomics, CESG,
unknown function; NMR {Arabidopsis thaliana} SCOP:
b.1.25.1
Length = 151
Score = 25.3 bits (55), Expect = 5.7
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 18/67 (26%)
Query: 33 KHQNFVSEPMG--EKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNP 90
K ++FV++ + KP + V D+ +S + ++ NP
Sbjct: 7 KAKDFVADKLTAIPKPEGSVTDV-DLKDVNRDSVEYLAKVS---------------VTNP 50
Query: 91 NSLPIPI 97
S IPI
Sbjct: 51 YSHSIPI 57
>2qv5_A AGR_C_5032P, uncharacterized protein ATU2773; structural
genomics, unknown function, PSI-2, protein struct
initiative; 1.90A {Agrobacterium tumefaciens str}
Length = 261
Score = 25.4 bits (55), Expect = 6.6
Identities = 5/31 (16%), Positives = 13/31 (41%)
Query: 12 TVHFWPFTSPTQELAKMSTSQKHQNFVSEPM 42
T+ F + Q + + + H+ + P+
Sbjct: 58 TLGFAASGNSLQRWMQDARREGHEILLQIPL 88
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 25.7 bits (57), Expect = 6.7
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 44 EKPVTELAGVGDVLGKRLESKG 65
+ GVG K+L+ G
Sbjct: 114 STDIQYAKGVGPNRKKKLKKLG 135
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex,
Y-family DNA polym translesion synthesis, nucleoside
triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens}
PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A*
2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A*
3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A*
...
Length = 420
Score = 25.4 bits (56), Expect = 7.8
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 45 KPVTELAGVGDVLGKRLESKG 65
+ E+ G+G K LE+ G
Sbjct: 234 NHIKEIPGIGYKTAKCLEALG 254
>1yyc_A LEA protein, putative late embryogenesis abundant protein;
structural genomics, protein structure initiative,
CESG; NMR {Arabidopsis thaliana}
Length = 174
Score = 25.0 bits (54), Expect = 8.4
Identities = 14/67 (20%), Positives = 21/67 (31%), Gaps = 18/67 (26%)
Query: 33 KHQNFVSEPMG--EKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNP 90
K + F +E + P + V D G + + + KNP
Sbjct: 30 KAKGFFAEKLANIPTPEATVDDV-DFKGVTRDGVDYHAK---------------VSVKNP 73
Query: 91 NSLPIPI 97
S IPI
Sbjct: 74 YSQSIPI 80
>1y56_B Sarcosine oxidase; dehydrogenase, protein-protein complex,
oxidoreductase; HET: FAD FMN ATP CXS; 2.86A {Pyrococcus
horikoshii}
Length = 382
Score = 24.8 bits (55), Expect = 9.4
Identities = 11/82 (13%), Positives = 22/82 (26%), Gaps = 19/82 (23%)
Query: 22 TQELAKMS--------TSQKHQNFVSEPMGEKPVTELAGVGDVLGK---RLESKG----- 65
+ M+ KHQ +++P+ + + G G
Sbjct: 205 ANLINAMAGIKTKIPIEPYKHQAVITQPIKRGTI-NPMVISFKYGHAYLTQTFHGGIIGG 263
Query: 66 FDKSINP--QMFPDPDIEEKVL 85
I P + P + +V
Sbjct: 264 IGYEIGPTYDLTPTYEFLREVS 285
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.134 0.422
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,035,013
Number of extensions: 109471
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 185
Number of HSP's successfully gapped: 21
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.3 bits)